Related papers: Atomic Density Distributions in Proteins: Structur…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
The rigidity and flexibility of homologous psychrophilic(P), mesophilic(M) and thermophilic(T) proteins have been investigated at the global and local levels in terms of packing factor and atomic fluctuations obtained from B-factors. For…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Packing problems have been a source of fascination for millenia and their study has produced a rich literature that spans numerous disciplines. Investigations of hard-particle packing models have provided basic insights into the structure…